Introduction to GSAS & GSAS-II R.B. Von Dreele, APS, Argonne National Laboratory, USA [email protected] Presented at 44 th Course: The Power of Powder.

Introduction to GSAS & GSAS-II

R.B. Von Dreele, APS, Argonne National Laboratory, [email protected]

Presented at 44th Course: The Power of Powder Diffraction, Erice, Italy, 2-12 June, 2011

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A bit of history

GSAS – conceived in 1982-1983 by A.C. Larson & R.B. Von Dreele1st version released in Dec. 1985

• Designed for multiple data (histograms) & phases – “Premise of GSAS”

• Did single crystal & powders from start• Only TOF neutrons (& buggy) • Objective – a tool to give to users at LANSCE for diffraction –

can take home & do it themselves!• Only for VMS - VAXFortran • Was “OOP” before OOP invented• Coherent data structure (ISAM for EXP file)• Complexity of multidata/phases – required a “smart” control

file editor - EXPEDT

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A bit more of historyLater – add CW neutrons & CW x-rays (powder data)

SGI unix version & then PC (MS-DOS) versionalso Linux version (briefly HP UX version)

2001 – EXPGUI developed by B.H. TobyRecent – spherical harmonics texture & proteins

New Windows, MacOSX, Fedora & RedHat linux versionsAll identical code – g77 Fortran; 50 pgms. & ~800 subroutinesGrWin & X graphics via pgplotEXPGUI – all Tcl/Tk – user additions welcome

Basic structure is essentially unchanged 20+ yrs later

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Structure of GSAS

1. Multiple programs - each with specific purposeediting, powder preparation, least squares, etc.

2. User interface – EXPEDT – control file complexityedit control data & problem parameters forcalculations - multilevel menus & help listingstext interface (no mouse!)visualize “tree” structure for menus

3. Common file structure – all named as “experiment.ext”experiment name used throughout, extensiondiffers by type of file

4. Graphics - both screen & hardcopy5. EXPGUI – graphical interface (windows, buttons, edit boxes, etc.); incomplete overlap with EXPEDT but with useful extra features – by B. H. Toby

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GSAS & EXPGUI interfaces

EXPEDT data setup option (<?>,D,F,K,L,P,R,S,X) >EXPEDT data setup options: <?> - Type this help listing D - Distance/angle calculation set up F - Fourier calculation set up K n - Delete all but the last n history records L - Least squares refinement set up P - Powder data preparation R - Review data in the experiment file S - Single crystal data preparation X - Exit from EXPEDT

On console screenKeyboard input – text & numbers1 letter commands – menu helpLayers of menus – tree structureType ahead thru layers of menusMacros ($M, $R & $X commands)

GSAS – EXPEDT (and everything else):

Numbers – real: ‘0.25’, or ‘1/3’, or ‘2.5e-5’ all allowedDrag & drop for file names

EXPEDT – very complex; error checking; ask questions ONCE; & don’t ask what user shouldn’t have to know (symmetry operators, form factors, etc.) – result of the “Premise”

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GSAS Macro files (example)

Add some atoms in expedt – starts at opening prompt & ends by terminating expedt; includes setting scale factor & some other stuff A bit cryptic?

k l a !We need to insert the atomsi 10 sb 0 0 0 1 Sb i / !Enter the Antimony atomi n o 1/4 1/4 1/4 1 O i / !Enter the Oxygen atomi n f .064 .136 .394 1 F i / ! and the Fluorine atomv 10:12 x u !Refine both position and Thermal motionx !We are finished with the atomso h !Let's set the histogram scale factor up properlyc .4 !Change it to .4x x !Exit back to the main LS menul !Edit the LS control datac 5 !Run 5 cyclesf n !Refine on F, not FSQs 1.5 / !Limit the data to F>3Sig(F)n 5 !Set Rfree on 5% of datax !We are done with the LS control editingx !We are done with the LS data editingx !Exit from EXPEDT

Comments on each line after “!”

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PC-GSAS – GUI only for access to GSAS programs

pull down menus for GSAS programs

(Windows only - not linux)

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GSAS & EXPGUI interfaces

EXPGUI:Access to GSASTypical GUI – edit boxes,buttons, pull downs etc.Liveplot – powder pattern

GSAS-II: A fresh start

GSASII – fresh start

Fill in what’s missing from GSAS:- Indexing- Structure solutionBase code – pythonMixed in old GSAS FortranGraphics – matplotlib,OpenGLGUI – wxPythonMath – numpy,scipyCurrent: python 2.6 & 2.7

Brief demo?

GSAS-II: A new General Structure Analysis System Goals:

– Cover crystallographic data analysis from raw data to final result– Same premise as for GSAS; combined data analysis– A complete system in a modern, easily accessible computer

language – Python– Modern Graphical User Interface (GUI)– Open source – Python– All modern platforms (Windows, Linux & Mac OS10+) – Python– Reuse a bit of old GSAS – Fortran; e.g. space group stuff– Presently aimed at x-ray scattering : include neutrons in future – More “General” – include small angle, PDF, reflectrometries

GSAS-II: A screen shot – 3 frame layout

Data tree

Data window

Graphics window

Data tabs

Main menu

Submenu

Drawing tabs

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Another screen shot of GSAS-II – multipattern peak fitting

Console – output messagesConsole – list output

Progress bar

Data tree

Data items – peak list

GSAS-II Current capabilities: 2D imagesCalibration – tilted detector (e.g. 45 about vertical axis)

Ellipses – sections of Debye-Scherrer cones

Ellipse centers – not on beam center!

Fitting only requires material (LaB6) and l (e.g. don’t need to know distance – get that from fit)

Choice of color scheme – “Paired” is shown

GSAS-II Current capabilities: 2D imagesIntegration

Multiple pie shaped sections with definable starting azimuth

Lower & upper limits on 2QMasks – spots, arcs, rings & polygons (not shown)Effective replacement for Fit2D

Unlimited workspaces – as many images as you want.Image combination – sum/differenceImage formats – tiff, MAR345, e.g. all I could find at APS.

GSAS-II Current capabilities: Powder patterns

Waterfall plots or contour plots

Peaks can be selected/fitted & indexed to identify lattice – modification of algorithm by A. Coelho.

GSAS-II Current capabilities: Pair Distribution Functions

Multiple PDFs – example: 183 images/183 powder patterns/183 G(R)s calculatedShows transition as T varied

Simple interface – one for each PDF; easy controls

GSAS-II More capabilities:Structure drawing

PolyhedraVan der Waals Balls & sticksThermal ellipsoidsAll selectable by atom

GSAS-II Future – fill in rest of the maze Pawley/le Bail

refinement Charge flipping Monte Carlo/Simulated

Annealing Rietveld refinement Result Analysis

– Bonds & angles– Validation

CIF Publication Other scattering

– PDF (done)– Small angle– ReflectometryNB – nonatomistic

models

GSAS & GSAS-II Availability

Subversion server at Argonne: https://subversion.xor.anl.aps.gov

GSAS & EXPGUI: find it under EXPGUI (don’t go to GSAS – that’s source for us only); easy installation/upgrade

Erice - //ERICE_SERVER/GSAS – Win, Linux & Mac OSX pyGSAS/trunk & pyGSAS/Examples

– But not much instruction for downloading/installing/running; hopefully soon

– You will need python 2.6-2.7, matplotlib, numpy, scipy, pyOpenGL, wxPython – easy from Enthought

Also Fprime & Absorb: find under pyFprime A plug for APS & 11BM – go to http://11bm.xor.aps.anl.gov12 detector/analyzer diffractometer with mail-in program…